Contacts of the helix formed by residues 240 - 261 (chain B) in PDB entry 1QK1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLY 3.6 10.7 + - - -
115B TYR* 4.0 35.2 + - + +
118B GLU* 4.5 1.3 + - - +
124B SER* 4.1 1.6 + - - -
236B GLU* 3.8 16.5 + - - +
237B LYS 5.3 0.2 + - - -
238B GLY* 3.8 1.8 - - - -
239B GLY* 1.3 74.4 - - - +
241B MET* 1.3 63.8 + - - +
242B LYS* 3.7 6.7 - - - +
243B ARG* 3.1 54.3 + - - +
244B VAL* 3.1 18.7 + - - +
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Residues in contact with MET 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLY 3.0 7.2 + - - +
116B PHE* 3.6 21.3 - - + -
124B SER* 4.1 12.1 + - - +
125B ARG 4.3 1.1 - - - +
126B VAL* 3.8 24.2 - - - -
239B GLY 2.9 8.5 + - - -
240B ASN* 1.3 72.3 - - - +
242B LYS* 1.3 63.2 + - - +
244B VAL* 3.1 7.7 + - - +
245B PHE* 2.9 22.5 + - - +
288B ALA* 4.5 3.1 - - + -
289B GLY 3.5 36.3 - - - +
290B VAL* 4.0 15.7 - - + -
345B VAL* 4.2 12.3 - - + -
348B VAL* 4.4 11.9 - - + -
349B ILE* 4.0 23.3 - - + -
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Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 3.7 15.6 + - - -
109B SER* 4.7 5.3 + - - +
111B ILE* 3.3 36.7 + - + -
112B ARG* 5.2 0.2 - - - +
113B SER 3.6 20.4 - - - +
114B GLY* 3.0 18.0 + - - +
240B ASN* 3.1 6.9 - - - +
241B MET* 1.3 78.4 - - - +
243B ARG* 1.3 61.5 + - - +
245B PHE* 3.3 5.8 + - - +
246B GLU* 3.0 56.0 + - + +
345B VAL* 6.3 0.2 - - - -
349B ILE* 5.5 0.2 - - - -
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Residues in contact with ARG 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TYR* 5.8 1.2 + - - -
236B GLU* 2.7 39.7 + - - +
237B LYS 5.5 1.4 + - - -
240B ASN* 3.1 37.5 + - - +
242B LYS* 1.3 79.1 - - - +
244B VAL* 1.3 62.9 + - - +
246B GLU* 3.2 15.7 + - + +
247B ARG* 3.1 31.6 + - + +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B SER* 4.0 16.2 - - - +
125B ARG* 4.2 5.4 - - - +
126B VAL* 3.9 21.1 - - + +
234B SER* 2.8 51.3 + - - +
236B GLU* 3.7 34.3 - - + +
240B ASN 3.1 13.4 + - - +
241B MET* 3.4 10.8 - - - +
243B ARG* 1.3 77.0 - - - +
245B PHE* 1.3 56.9 + - - +
247B ARG* 3.5 6.9 + - - +
248B PHE* 3.0 15.6 + - - +
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Residues in contact with PHE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP 4.7 0.2 - - - -
106B LEU* 5.0 0.2 - - + -
108B ALA* 3.9 14.8 - - + -
111B ILE* 3.8 30.7 - - + -
126B VAL* 4.4 9.4 - - + -
241B MET 2.9 16.7 + - - +
242B LYS* 3.8 5.6 - - - +
244B VAL* 1.3 77.8 - - - +
246B GLU* 1.3 59.7 + - - +
248B PHE* 3.3 33.3 - + + +
249B CYS* 2.9 46.2 + - - -
286B LEU* 4.6 1.8 - - + -
341B GLU* 4.1 24.7 - - + -
342B VAL* 4.2 13.5 - - + -
345B VAL* 3.7 38.6 - - + -
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Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA* 3.7 26.0 - - + +
109B SER* 5.1 2.6 + - - -
242B LYS* 3.0 51.8 + - + +
243B ARG* 3.8 16.2 - - + +
245B PHE* 1.3 75.7 - - - +
247B ARG* 1.3 57.8 + - - +
249B CYS* 3.4 1.7 + - - +
250B ARG* 2.9 36.9 + - - +
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ASP* 4.5 13.2 + - - -
164B LEU* 4.4 15.0 - - + -
215B ASN* 4.6 7.0 - - - +
217B GLU* 4.3 7.4 + - - -
219B SER* 3.3 37.8 + - - -
220B PHE* 4.1 9.3 - - + -
234B SER* 3.5 13.3 + - - +
235B MET 3.3 25.5 + - - -
236B GLU* 3.1 33.3 + - - +
243B ARG* 3.1 23.9 + - + +
244B VAL* 3.8 7.4 - - - +
246B GLU* 1.3 73.0 - - - +
248B PHE* 1.3 60.9 + - - +
250B ARG* 3.8 17.6 - - - +
251B GLY* 2.9 28.4 + - - -
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.3 9.2 - - + -
126B VAL* 3.7 38.8 - - + -
128B THR* 3.5 39.0 - - + -
130B ARG* 5.5 0.9 - - - -
220B PHE* 4.3 5.2 - - - -
232B VAL* 4.1 14.1 - - + -
234B SER* 3.9 15.2 + - - -
244B VAL 3.0 16.1 + - - +
245B PHE* 3.3 31.0 - + - +
247B ARG* 1.3 77.5 - - - +
249B CYS* 1.3 66.0 + - - +
251B GLY* 3.5 0.7 + - - -
252B LEU* 3.1 42.0 + - + +
286B LEU* 3.8 19.5 - - + -
341B GLU* 5.9 0.2 - - - -
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Residues in contact with CYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 3.3 42.2 - - + +
108B ALA* 4.0 9.9 - - + +
245B PHE* 2.9 55.6 + - - +
246B GLU 3.9 3.1 - - - +
248B PHE* 1.3 79.1 - - - +
250B ARG* 1.3 63.6 + - - +
252B LEU* 3.5 4.4 + - - +
253B LYS* 3.2 31.9 + - - +
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASP* 2.6 45.3 + - - -
164B LEU* 4.3 18.4 - - + +
246B GLU* 2.9 25.0 + - - +
247B ARG* 3.8 23.5 - - - +
249B CYS* 1.3 75.4 - - - +
251B GLY* 1.3 65.2 + - - +
253B LYS* 3.3 7.8 + - - +
254B GLU* 3.1 25.3 + - + +
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 5.8 0.4 - - - -
164B LEU* 3.8 20.1 - - - +
220B PHE* 3.7 22.2 - - - -
247B ARG 2.9 16.3 + - - -
250B ARG* 1.3 78.0 - - - +
252B LEU* 1.3 55.9 + - - +
254B GLU* 3.3 1.9 + - - +
255B VAL* 2.9 34.0 + - - +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.6 15.3 - - + -
128B THR* 4.1 2.5 - - + -
130B ARG* 3.7 40.2 - - + +
220B PHE* 4.3 0.6 - - - -
232B VAL* 4.1 33.7 - - + -
248B PHE* 3.1 54.0 + - + +
249B CYS* 4.0 4.3 - - - +
250B ARG 3.3 0.2 - - - -
251B GLY* 1.3 75.7 - - - +
253B LYS* 1.3 59.1 + - - +
255B VAL* 3.5 7.4 + - + +
256B GLU* 3.0 30.2 + - - +
266B PHE* 4.6 9.0 - - + -
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Residues in contact with LYS 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 3.1 49.4 + - + -
107B ASP* 4.4 7.7 + - - +
108B ALA 5.4 0.2 - - - +
249B CYS* 3.2 19.9 + - - +
250B ARG* 3.9 5.8 - - - +
252B LEU* 1.3 77.0 - - - +
254B GLU* 1.3 59.5 + - - +
256B GLU* 3.5 10.7 + - - +
257B ARG* 3.0 28.8 + - - +
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Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B GLY 5.6 0.5 - - - +
160B LEU* 3.6 25.1 - - + -
161B LYS 6.0 0.7 - - - +
164B LEU* 4.4 9.0 - - + -
250B ARG* 3.1 19.5 + - + +
251B GLY* 3.6 6.7 - - - +
253B LYS* 1.3 77.2 - - - +
255B VAL* 1.3 63.4 + - - +
257B ARG* 2.3 47.1 + - - +
258B LEU* 3.1 30.3 + - + +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B VAL* 6.1 3.6 - - + -
156B ALA* 4.9 4.3 - - + -
157B LEU* 3.9 29.4 - - + -
160B LEU* 4.2 15.0 - - + -
220B PHE* 5.1 2.2 - - + -
222B ILE* 4.7 10.8 - - + -
251B GLY 2.9 22.5 + - - +
252B LEU* 3.9 9.4 - - + +
254B GLU* 1.3 75.8 - - - +
256B GLU* 1.3 61.7 + - - +
258B LEU* 3.3 8.6 + - + +
259B ILE* 3.1 31.8 + - + +
266B PHE* 4.4 16.6 - - + -
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 6.0 1.7 - - - +
252B LEU 3.0 18.5 + - - +
253B LYS* 3.9 10.3 - - - +
255B VAL* 1.3 75.0 - - - +
257B ARG* 1.3 66.0 + - - +
259B ILE* 3.4 8.7 + - + +
260B GLN* 3.0 55.5 + - + +
265B GLU* 6.4 0.2 - - - -
266B PHE* 3.6 37.6 + - + +
274B TYR* 4.9 8.9 + - - -
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Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B GLY 5.5 2.0 + - - -
253B LYS 3.0 15.6 + - - +
254B GLU* 2.3 42.7 + - - +
255B VAL 3.2 0.2 - - - -
256B GLU* 1.3 77.3 - - - +
258B LEU* 1.3 83.5 + - - +
260B GLN* 3.3 9.6 + - - +
261B GLU* 3.1 50.6 + - - +
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ALA* 3.2 38.0 - - + +
159B GLY* 3.8 27.4 - - - +
160B LEU* 3.9 15.3 - - + -
254B GLU* 3.1 19.4 + - - +
255B VAL* 3.7 5.6 - - - +
257B ARG* 1.3 105.7 - - - +
259B ILE* 1.3 61.8 + - - +
261B GLU* 3.4 33.8 - - - +
262B ARG* 3.9 11.1 + - - +
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Residues in contact with ILE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ILE* 4.2 12.3 - - + -
152B VAL* 4.4 16.4 - - + +
153B VAL* 5.4 2.7 - - + -
156B ALA* 3.5 23.1 - - + -
255B VAL* 3.1 18.0 + - + +
256B GLU* 3.4 12.8 - - + +
258B LEU* 1.3 73.3 - - - +
260B GLN* 1.3 67.3 + - + +
261B GLU 3.1 2.2 - - - -
262B ARG* 3.2 13.7 + - - +
263B GLY 3.4 0.2 + - - -
264B TRP* 3.0 44.0 + - + +
265B GLU* 4.1 10.8 - - - -
266B PHE* 3.7 36.8 - - + +
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Residues in contact with GLN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B GLU* 3.0 42.1 + - + +
257B ARG* 3.7 8.0 - - - +
258B LEU 3.3 0.4 - - - -
259B ILE* 1.3 76.4 - - + +
261B GLU* 1.3 65.7 + - - +
263B GLY 3.1 9.1 + - - -
264B TRP 3.3 16.2 - - - +
265B GLU* 4.3 25.0 + - - +
15C TYR* 4.5 3.3 + - - -
31C PRO* 3.6 22.1 - - + +
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Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ARG* 3.1 38.4 + - - +
258B LEU* 3.4 27.5 - - - +
259B ILE 3.1 0.2 - - - -
260B GLN* 1.3 79.1 - - - +
262B ARG* 1.3 67.1 + - + +
263B GLY 3.3 0.8 + - - -
15C TYR* 4.3 8.8 - - - -
16C PRO 5.0 1.9 - - - +
17C ASP* 5.3 0.9 - - - +
18C LEU 5.4 2.4 + - - -
19C ARG* 3.4 46.6 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il